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Originally Posted by Mr.Deflok
I'm about to leave for work so I'll answer these as quick as I can, or at least as well as I think...
1. They were re-inserted into the source so that the cycle of Zion's destruction could happen
2. No, since the anomaly has chosen not to fulfill his purpose the cycle of the Matrix has been disturbed, yet, it is still possible.
3. The machines control themselves, they're highly advanced AI, sentient being as it were.
4. Why do some people possess slight telekinetic powers? It's anomalous and since Neo has the ability in the Matrix it would only make sense that his physical self would do too.
Very quick and very brief, still half asleep and needing to get to work.
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Well you seem to have answered these questions for yourself, but non of these are explicitly laid out in Revolutions. You have drawn your own conclusions, which is fine, but I don't believe that any of these were actually directly addressed in the movie.